S. Darko follows Samantha Darko, the younger sister of Donnie, the protagonist of Donnie Darko, and her friend Corey. On their way to California, their car breaks down, forcing them to wait in a small town until it is fixed. While there, Samantha begins to have dreams that warn her of the end of the universe.

After narrowly escaping a bizarre accident, a troubled teenager is plagued by visions of a large bunny rabbit that manipulates him to commit a series of crimes.

Maltazard, the Evil M, is now 7 feet tall and evolving among the humans, causing terror wherever he goes. His goal is simple: forming an army of giant henchmen and ruling over the universe. Meanwhile, Arthur is still a Minimoy, and thus in a state where he’s unable to fend him off. With the help of Selenia and Betameche, he hatches a plan to regain his usual size: all they must do is infiltrate Arthur’s house through the pipeworks, catch an electric train from his bedroom to his grandfather’s study and find an elixir that will make him grow back to his human size. Sounds simple enough, if it weren’t for Darkos, Maltazard’s own son, hot on their tails.

When the five puppies stumble upon the Five Power Rings of Inspiron (alien artifacts abandoned on Earth 16 years ago), they all develop super powers, and are enlisted in Captain Canine’s battle against the evil Darkon alien Commander Drex. Captain Canine is commander of space ship Megasis and is from the planet Inspiron. He is the mortal enemy of the Commander Drex. In charge of protecting Princess Jorala and the Five Power Rings from Drex, Megasis places the rings in hiding on the planet Earth, and takes the form of a German Shepherd, intending to stay on earth in very deep cover. Adopted by aspiring young comic book artist Ian Shaeffer, and renamed Captain Canine, he spends 16 happy years on Earth, as Ian recounts the stories of his space adventures. But when the five Buddies discover the Power Rings and instantly develop superpowers, Captain Canine has to train them very quickly indeed – for Commander Drex is headed back to earth, and this time he’s determined to succeed.